Recent papers (with PDF files) resulting from the group (Folding@Home)

Publications of work performed at MIT (1992-1996):

  1. V. S. Pande, A. Yu. Grosberg, and T. Tanaka.  Non-Randomness in Protein Sequences: Evidence for a Physically Driven Stage of Evolution? Proceeding of the National Academy of Science, U.S.A., 91, 12972 (1994)
  2. V. S. Pande, A. Yu. Grosberg, and T. Tanaka. Thermodynamic Procedure to Synthesize Heteropolymers that can Renature to Recognize a Given Target Molecule. Proceeding of the National Academy of Science, U.S.A., 91, 12976 (1994)
  3. V. S. Pande, C. Joerg, A. Yu. Grosberg, and T. Tanaka.  Enumeration of the Hamiltonian Walks on a Cubic Sublattice. Journal of Physics, A27, 6231 (1994)
  4. V. S. Pande, A. Yu. Grosberg, and T. Tanaka.  Phase Diagram of Imprinted Copolymers, Journal of Physics (Paris), 4, 1771 (1994)
  5. V. S. Pande, A. Yu. Grosberg, and T. Tanaka.  Folding Thermodynamics and Kinetics of Imprinted Renaturable Heteropolymers, Journal of Chemical Physics, 101, 8246 (1994)
  6. V. S. Pande and  C. Joerg,  Enumeration of the Hamiltonian Walks on a Sublattice, Student Workshop on Scalable Computing, MIT/LCS/TR-622, 53 (1994)
  7. V. S. Pande, A. Yu. Grosberg, and T. Tanaka.  Freezing Transition of Random Heteropolymers Consisting of an Arbitrary Set of Monomers.  Physical Review, E51, 3381 (1995)
  8. V. S. Pande, A. Yu. Grosberg, and T. Tanaka, Phase Diagram of Heteropolymers with an Imprinted Conformation. Macromolecules, 28, 2218 (1995)
  9. V. S. Pande, A. Yu. Grosberg, and T. Tanaka.  Freezing Transition of an Imprinted Copolymer in a Random External Field. Journal of Physics A28, 3657 (1995)
  10. V. S. Pande, A. Yu. Grosberg, and T. Tanaka. How Accurate Must Potentials Be for Successful Modeling of Protein Folding? Journal of Chemical Physics 103, 9482 (1995)
  11. T. Tanaka, C-n Wang, A. English, S. Masamune, H. Gold, R. Levy, K. King, V. S. Pande, and A. Yu. Grosberg.  Polymer Gels that can Recognize and Recover Molecules.  Faraday Discussions, 101, 201-206 (1995)
  12. V. S. Pande, A. Yu. Grosberg,  C. Joerg, and T. Tanaka.  How Well is Heteropolymer Freezing Described by the Random Energy Model?  Physical Review Letters, 76, 3987-3990 (1995)
  13. V. S. Pande, A. Yu. Grosberg, M. Kardar,  C. Joerg, and T. Tanaka.  Polyampholyte Freezing Transition.  Physical Review Letters, 77, 3565-3568 (1996)
  14. V. S. Pande, A. Yu. Grosberg, and T. Tanaka.  On the Theory of Folding Kinetics for Short Proteins.  Folding and Design  2, 109 (1997)
  15. V. S. Pande and J. Onuchic.  Electron Transport  in Disordered Polymeric Systems.  Physical Review Letters  78, 146 (1997)
  16. V. S. Pande, A. Yu. Grosberg, and T. Tanaka. How to make Heteropolymers which can Renature to Recognize a Given Target Molecule, 107  316 Physica D  (1997)
  17. V. S. Pande, A. Yu. Grosberg, and T. Tanaka.  Statistical Mechanics of Simple Models of Protein Folding. Biophysical Journal    73,  3192-3210 (1997)
  18. V. S. Pande, A. Yu. Grosberg, and T. Tanaka.  Thermodynamics of the coil to frozen globule transition in heteropolymers.  Journal of Chemical Physics  107, 5118-5124 (1997)
  19. M. Tanaka, A. Yu. Grosberg, V. S. Pande, and T. Tanaka.  Molecular Dynamics Study of the Structural Organization of a Strongly-Coupled Chain of Charged Particles. Physical Review E 56  5798-5808 (1997)

Publications of work performed at UC Berkeley (1996-1999):

  1. A. Chakraborty, E. I. Shakhnovich, and V. S. Pande.  Broken Ergodicity in Compact Random Heteropolymers with  Correlated Sequence Fluctuations. Journal of Chemical Physics . 108, 1683-1687  (1997)
  2. R. Du, V. S. Pande, A. Yu. Grosberg, T. Tanaka, and E. I. Shakhnovich. On the Transition Coordinate for Protein Folding.  Journal of Chemical Physics  108,  334-350  (1998)
  3. V. S. Pande and D. S. Rokhsar.  Is the Molten Globule a third Phase of Proteins?  Proceedings of the National Academy of Science, USA 95  1490-1494    (1998)
  4. V. S. Pande, A. Yu. Grosberg, and T. Tanaka, D. S. Rokhsar.  Protein Folding Pathways: Is a “new view” needed?  Current Opinions in Structural Biology  8  68-79 (1998)
  5. V. S. Pande and D. S. Rokhsar. Folding Pathway of a Lattice Model for Protein Folding.  Proceedings of the National Academy of Science, USA 96,  1273-1278  (1999)
  6. R. Du, V. S. Pande, A. Yu. Grosberg, T. Tanaka, and E. I. Shakhnovich.  On the Role of Conformational Geometry in Protein Folding.  111,  10375-10380  Journal of Chemical Physics  (1999)
  7. A. Golumbfskie, V. S. Pande, and A. Chakraborty.  Simulation of biomimetic recognition between polymers and surfaces.  Proceedings of the National Academy of Science, USA,  96, 11707-11712  (1999)
  8. V. S. Pande and D. S. Rokhsar.  Molecular dynamics simulation of unfolding and refolding of a b-hairpin.  Proceedings of the National Academy of Science, USA  96  9062-9067  (1999)
  9. Z. Bryant, V. S. Pande, and D. S. Rokhsar.  Mechanical unfolding of a beta hairpin using molecular dynamics.  Biophysical Journal, 78, 584-589, (2000)
  10. V. S. Pande, A. Yu. Grosberg, and T. Tanaka.  Heteropolymer Freezing and Design:  Towards Physical Models of Protein Folding.  Reviews of Modern Physics  72, 259-286 (2000)
  11. R. Anderson, V. S. Pande, and C. Radke. Dynamic lattice Monte Carlo simulation of a model protein at an oil-water interface.  Journal of Chemical Physics, 112, 9167-9185 (2000)

Publications of work performed at Stanford University (1999-present):
  1. M. R. Shirts and V. S. Pande. Screen Savers of the World, Unite! Science, 290, 1903-1904 (2000)
  2. S. Elmer and V. S. Pande. A new twist on the helix-coil transition: a non-biological polymer with protein-like intermediates. Journal of Physical Chemistry B, 105, 482-485 (2001)
  3. M. R. Shirts and V. S. Pande. Mathematical Foundations of Ensemble Dynamics. Physical Review Letters, 86, 4983-4987 (2001)
  4. B. Zagrovic, E. Sorin, and V. S. Pande. Atomistic folding simulations of a beta hairpin. Journal of Molecular Biology 313, 151-169 (2001)
  5. V. S. Pande, I. Baker, J. Chapman, S. P. Elmer, S. Khaliq, S. M. Larson, Y. M. Rhee, M. R. Shirts, C. Snow, E. Sorin, B. Zagrovic. Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing. Kollman Memorial Issue, Biopolymers, 68(1), 91-109 (2003)
  6. E. Sorin, M. Engelhardt, D. Herschlag, and V. S. Pande. Unfolding simulations of a GNRA tetraloop. Journal of Molecular Biology, 317, 493-506 (2002)
  7. R. Russell, I. S. Millet, M. W. Tate, L. W. Kwok, B. Nakatani, S. M. Gruner, S. G. J. Mochrie, V. S. Pande, S. Doniach, D. Herschlag, and L. Pollack. Rapid Compaction During RNA Folding. Proceedings of the National Academy of Science, USA, 99, 4266-4271 (2002)
  8. B. Zagrovic, C. Snow, S. Khaliq, M. Shirts, and V. S. Pande. Native-like mean structure in the unfolded ensemble of small proteins. Journal of Molecular Biology323, 153-164 (2002)
  9. C. Snow, H. Nguyen, V. S. Pande, and M. Gruebele. Folding of a bba protein: simulation and theory. Nature, 420, 102-106 (2002)
  10. B. Zagrovic, C. D. Snow, M. R. Shirts and V. S. Pande. Simulation of Folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing. Journal of Molecular Biology, 323, 927-937 (2002)
  11. S. M. Larson, J. England, J. DesJarlais, and V. S. Pande. Thoroughly sampling sequence space: large-scale protein design of structural ensembles. Protein Science11 2804-2813 (2002)
  12. Y. M. Rhee and V. S. Pande. Multiplexed Replica Exchange Molecular Dynamics Method for Protein Folding Simulation. Biophysical Journal, 84, 775–786 (2003)
  13. C. Snow, B. Zagrovic, and V. S. Pande. The Trp Cage: Folding Kinetics and Unfolded State Topology via Molecular Dynamics Simulations. Journal American Chemical Society, 124, 14548-14549 (2002)
  14. A. I. Jewett, V. S. Pande, and K. W. Plaxco. Cooperativity, smooth energy landscapes and the origins of topology-dependent protein folding rates. Journal of Molecular Biology, 326 247-253 (2003)
  15. S. M. Larson, A. Garg, J. DesJarlais, and V. S. Pande. Increased detection of structural templates using alignments of designed sequences. Proteins: Structure, Function, and Genetics51 390-396 (2003)
  16. B. Zagrovic and V. S. Pande. Solvent Viscosity Dependence of the Folding Rate of a Small Protein: a Distribut ed Computing Study. Journal of Computational Chemistry, 24 1432–1436 (2003)
  17. E. Sorin, Y. M. Rhee, B. Nakatani, and V. S. Pande. Insights into nucleic acid hairpin conformational dynamics from massively parallel stochastic simulations. Biophysical Journal, 85 790-803 (2003)
  18. M. R. Shirts, J. W. Pitera, W. C. Swope, and V. S. Pande. Extremely Precise Free Energy Calculations of Amino Acid Side Chain Analogs: Comparison of Common Molecular Mechanics Force Fields for Proteins. Journal of Chemical Physics, 119 5740-5761 (2003)
  19. S. M. Larson and V. S. Pande. Sequence optimization for native state stability determines the evolution and folding kinetics of a small protein. Journal of Molecular Biology, 332 275-286 (2003)
  20. S. M. Larson, C. Snow, V. S. Pande. Folding@Home and Genome@Home: Using distribut ed computing to tackle previously intractable problems in computational biology. Modern Methods in Computational Biology, R. Grant, ed, Horizon Press (2003)
  21. M. R. Shirts, E. Bair, G. Hooker, and V. S. Pande. Equilibrium free energies from nonequilibrium measurements using maximum likelihood methods. Physical Review Letters, 91 (2003)
  22. B. Zagrovic and V. S. Pande. How Can Proteins be Unfold ed and yet Have Native-like Properties: Structural Correspondence between the Alpha Helix and the Random-Flight Chain. Nature Structural Biology, 10 955-961(2003)
  23. V. S. Pande. Meeting half way on the bridge between protein folding theory and experiment. Proceedings of the National Academy of Sciences, USA, 100 3555-3556 (2003)
  24. P. Lenz, B. Zagrovic, J. Shapiro, and V. S. Pande. Folding probabilities: a novel approach to folding transitions. Journal of Chemical Physics, 120 6769-6778 (2003)
  25. E. Sorin, B. Nakatani, Y. M. Rhee, G. Jayachandran, V. Vishal, and V. S. Pande. Does Native State Topology Determine the RNA Folding Mechanism? Journal of Molecular Biology 337 789-797 (2003)
  26. Y. M. Rhee, E. J. Sorin, G. Jayachandran, E. Lindahl, V. S. Pande. Simulations of the role of water in the protein folding mechanism. Proceedings of the National Academy of Science, USA101 6456-6461 (2004)
  27. C. D. Snow, L. Qiu, D. Du, F. Gai, S. J. Hagen, and V. S. Pande. Tryptophan Zipper Folding Kinetics via Molecular Dynamics and Temperature Jump Spectroscopy. Proce edings of the National Academy of Sciences, USA, 101 4077-4082 (2004)
  28. P. Kasson and V. S. Pande. Molecular Dynamics Simulation of Lipid Reorientation at Bilayer Edges. Biophysical Journal, 86 3744-3749 (2004)
  29. N. Singhal, C. Snow, and V. S. Pande. Path sampling to build better roadmaps: predicting the folding rate and mechanism of a Trp Zipper beta hairpin. Journal of Chemical Physics121 415-425 (2004)
  30. V. S. Pande. Atomistic models of protein folding. Encyclopedia of Materials Research (2005)
  31. B. Zagrovic and V. S. Pande. How Does Averaging Affect Protein Structure Comparison on the Ensemble Level? Biophysical Journal 87 2240-6 (2004)
  32. J. E. Kohn, I. S. Millett, J. Jacob, B. Zagrovic, T. M. Dillon, N. Cingel, R. S. Dothager, S. Seifert, P. Thiyagarajan, T. R. Sosnick, M. Z. Hasan, V. S. Pande, I. Ruczinski, S. Doniach and K. W. Plaxco. Do the dimensions of chemically unfolded proteins differ significantly from the expectations of a random-coil model? Proceedings of the National Academy of Sciences, USA, 101 12491-6 (2004)
  33. S. Elmer and V. S. Pande. Foldamer simulations: Novel computational methods and applications to poly-phenylacetylene oligomers. Journal of Chemical Physics 121 12760-12771 (2004)
  34. V. S. Pande. Protein Aggregation and Disease: A universal TANGO? Nature Biotechnology22, 1240-1241 (2004)
  35. C. D. Snow, E. J. Sorin, Y. M. Rhee, and V. S. Pande. How well can simulation predict protein folding kinetics and thermodynamics? Annual Reviews of Biophysics34 43-69 (2005)
  36. L. T. Chong, C. D. Snow, Y. M. Rhee, and V. S. Pande. Dimerization of the p53 oligomerization domain: Identification of a folding nucleus by molecular dynamics simulations. Journal of Molecular Biology 345 869-78 (2004)
  37. S. Elmer and V. S. Pande. Length Dependent Folding Kinetics of poly-Phenylacetylene Oligomers: Structural Characterization of a Kinetic Trap, Journal of Chemical Physics122 124908 (2005)
  38. E. Sorin and V. S. Pande. Exploring the helix-coil transition via all-atom equilibrium ensemble simulations. Biophysical Journal88 2472-93 (2005)
  39. E. Sorin, Y. M. Rhee, and V. S. Pande. Does water play a structural role in the folding of small nucleic acids? Biophysical Journal88 2516-24 (2005)
  40. Y. M. Rhee and V. S. Pande. One-Dimensional Reaction Coordinate and the Corresponding Potential of Mean Force from Commitment Probability Distribution. Journal of Physical Chemistry B109 6780-6786 (2005)
  41. E. Sorin and V. S. Pande. Empirical force Field Assessment: the Interplay between van der Waals Scaling and Backbone Torsions. Journal of Computational Chemistry 26 682-690 (2005)
  42. M. R. Shirts and V. S. Pande. Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration. Journal of Chemical Physics 122 144107 (2005)
  43. M. R. Shirts and V. S. Pande. Solvation free energies of amino acid side chains for common molecular mechanics water models. Journal of Chemical Physics122 134508 (2005)
  44. D. Rother, G. Sapiro, and V. S. Pande. Statistical Characterization of Protein Ensembles. RECOMB (2005)
  45. Y. M. Rhee and V. S. Pande. On the role of chemical detail in simulating protein folding kinetics. Chemical Physics, in press (2005)
  46. S. Park, R. Radmer, T. Klein, V. S. Pande. New parameters for collagen simulation. Journal of Computational Chemistry, 26 1612-6 (2005)
  47. S. Elmer, S. Park, and V. S. Pande. PPA simulations in explicit solvent: 1. studying the role of solvaphobicity on foldamers assembly. Journal of Chemical Physics 123 114902 (2005)
  48. S. Elmer, S. Park, and V. S. Pande. Foldamer dynamics expressed via Markov State Models: 2. Explicit solvent molecular dynamics simulations in acetonitrile, chloroform, methanol, and water. Journal of Chemical Physics122 124908 (2005)
  49. B. Zagrovic, J. Lipfert, E. J. Sorin, I. S. Millett, W. F. van Gunsteren, S. Doniach and V. S. Pande. Unusual compactness of a polyproline type II structure. Proceedings of the National Academy of Science, USA, 102 11698-703 (2005)
  50. H. Fujutani, Y. Tanida, M. Ito, G. Jayachandran, C. Snow, M. R. Shirts, E. Sorin, and V. S. Pande. Direct calculation of the binding free energies of FKBP ligands using the Fujitsu BioServer massively parallel computer. Journal of Computational Physics,123 084108 (2005)
  51. N. Singhal and V. S. Pande. Error Analysis in Markovian State Models for protein folding. Journal of Chemical Physics,123 204909 (2005)
  52. B. Zagrovic, G. Jayachandran, I. S. Millett, S. Doniach and V. S. Pande. How large is alpha-helix in solution? Studies of the radii of gyration of helical peptides by SAXS and MD. Journal of Molecular Biology, 353 232-41 (2005)
  53. P. Petrone and V. S. Pande. Can conformational change be described by only a few normal modes? Biophysical Journal, 90 1583-93(2006)
  54. E. J. Sorin, Y. M. Rhee, M. R. Shirts, and V. S. Pande. The solvation interface is a determining factor in protein conformational preferences. Journal of Molecular Biology, 356 248-56 (2006)
  55. S. Park and V. S. Pande. How to validate Markovian Models. Journal of Chemical Physics124 54118(2006)
  56. L.T. Chong, W. C. Swope, J. W. Pitera, and V. S. Pande. A novel approach for computational alanine scanning: application to the p53 oligomerization domain. Journal of Molecular Biology, 357 1039-1049 (2006)
  57. G. Jayachandran, V. Vishal, and V. S. Pande. Folding Simulations of the Villin Headpiece in All-Atom Detail. Journal of Chemical Physics, in press (2006)
  58. C. Snow and V. S. Pande. Kinetic Definition of Protein Folding Transition State Ensembles and Reaction Coordinates. Biophysical Journal, in press (2006)
  59. E. Sorin and V. S. Pande. Nanotube confinement denatures proteins in confined spaces. JACS, in press (2005)
  60. I. Suydam, C. D. Snow, V. S. Pande and S. G. Boxer. Electric Fields at the Active Site of an Enzyme: Direct Comparison of Experiment with Theory. Science, in press (2006)
  61. G. Jayachandran, M. R. Shirts, S. Park, and V. S. Pande. Parallelized Over Parts Computation of Absolute Binding Free Energy with Docking and FEP. Journal of Chemical Physics, in press (2006)
  62. P. Kasson, N. Kelley, N. Singhal, M. Vrjlic, A. Brunger, and V. S. Pande. Sub-millisecond kinetics and intermediates of membrane fusion from molecular dynamics. Proceedings of the National Academy of Sciences, USA, in press (2006)
  63. Christophe Chipot, Vijay S. Pande, Alan E. Mark, and Thomas Simonson. “Significant applications of free energy calculations tochemistry and biology.” Ed., C. Chipot (2006)
  64. Vijay S. Pande, Eric J. Sorin, Christopher D. Snow, & Young Min Rhee. Protein “Folding Simulation.” Chapter to be published by the Royal Society, Ed. Victor Munoz (2006).

Last modified August 22, 2006